data_VL5
# 
_chem_comp.id                                    VL5 
_chem_comp.name                                  "(2S)-2-[(Z)-[1-(2-azanyl-1,3-thiazol-4-yl)-2-[[(2S)-3-methyl-1-oxidanylidene-3-(sulfooxyamino)butan-2-yl]amino]-2-oxidanylidene-ethylidene]amino]oxy-3-[4-[N-[(3R)-piperidin-3-yl]carbamimidoyl]phenoxy]propanoic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C25 H34 N8 O10 S2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "AIC499 (bound)" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2021-05-27 
_chem_comp.pdbx_modified_date                    2024-09-27 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        670.715 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VL5 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        7ONK 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_chem_comp.pdbx_pcm                              Y 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.alt_atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.charge 
_chem_comp_atom.pdbx_align 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_leaving_atom_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_chem_comp_atom.model_Cartn_x 
_chem_comp_atom.model_Cartn_y 
_chem_comp_atom.model_Cartn_z 
_chem_comp_atom.pdbx_model_Cartn_x_ideal 
_chem_comp_atom.pdbx_model_Cartn_y_ideal 
_chem_comp_atom.pdbx_model_Cartn_z_ideal 
_chem_comp_atom.pdbx_component_atom_id 
_chem_comp_atom.pdbx_component_comp_id 
_chem_comp_atom.pdbx_ordinal 
VL5 C10 C1  C 0 1 Y N N N N N -3.588  -16.865 -1.747  -5.873  -0.285 0.573  C10 VL5 1  
VL5 C11 C2  C 0 1 Y N N N N N -2.631  -16.946 -2.754  -5.011  -0.462 1.656  C11 VL5 2  
VL5 C12 C3  C 0 1 Y N N N N N -2.986  -16.742 -4.079  -3.861  0.291  1.749  C12 VL5 3  
VL5 C13 C4  C 0 1 Y N N N N N -4.311  -16.471 -4.397  -3.559  1.226  0.767  C13 VL5 4  
VL5 C14 C5  C 0 1 Y N N N N N -5.270  -16.390 -3.395  -4.416  1.405  -0.313 C14 VL5 5  
VL5 C15 C6  C 0 1 Y N N N N N -4.912  -16.589 -2.069  -5.564  0.651  -0.415 C15 VL5 6  
VL5 C17 C7  C 0 1 N N N N N N -3.721  -16.534 -6.740  -2.178  2.910  -0.183 C17 VL5 7  
VL5 C18 C8  C 0 1 N N S N N N -4.340  -16.107 -8.062  -0.865  3.645  0.095  C18 VL5 8  
VL5 C19 C9  C 0 1 N N N N N N -3.306  -16.196 -9.139  -0.919  4.269  1.466  C19 VL5 9  
VL5 C2  C10 C 0 1 N N N N N N -0.072  -15.834 -0.937  -10.298 -1.049 0.105  C2  VL5 10 
VL5 C24 C11 C 0 1 N N N N N N -7.156  -17.373 -9.680  2.538   2.576  -0.365 C24 VL5 11 
VL5 C25 C12 C 0 1 Y N N N N N -8.035  -17.019 -10.826 3.817   3.176  -0.804 C25 VL5 12 
VL5 C27 C13 C 0 1 Y N N N N N -8.657  -15.784 -12.598 5.977   3.083  -1.393 C27 VL5 13 
VL5 C3  C14 C 0 1 N N R N N N -1.086  -15.928 0.207   -9.182  -1.716 -0.702 C3  VL5 14 
VL5 C30 C15 C 0 1 Y N N N N N -9.206  -17.724 -11.158 3.958   4.498  -1.020 C30 VL5 15 
VL5 C31 C16 C 0 1 N N N N N N -7.450  -18.493 -8.786  2.475   1.136  -0.022 C31 VL5 16 
VL5 C34 C17 C 0 1 N N S N N N -8.921  -19.318 -7.031  3.556   -0.996 0.449  C34 VL5 17 
VL5 C35 C18 C 0 1 N N N N N N -8.222  -19.653 -5.697  4.726   -1.767 -0.167 C35 VL5 18 
VL5 C36 C19 C 0 1 N N N N N N -7.134  -18.625 -5.401  4.624   -1.713 -1.692 C36 VL5 19 
VL5 C37 C20 C 0 1 N N N N N N -7.631  -21.055 -5.823  6.045   -1.134 0.279  C37 VL5 20 
VL5 C39 C21 C 0 1 N N N N N N -10.355 -18.944 -6.815  3.656   -1.049 1.952  C39 VL5 21 
VL5 C4  C22 C 0 1 N N N N N N -1.948  -14.666 0.268   -9.608  -1.812 -2.170 C4  VL5 22 
VL5 C5  C23 C 0 1 N N N N N N -1.073  -13.421 0.305   -10.920 -2.598 -2.262 C5  VL5 23 
VL5 C6  C24 C 0 1 N N N N N N -0.134  -13.417 -0.896  -11.985 -1.905 -1.409 C6  VL5 24 
VL5 C8  C25 C 0 1 N N N N N N -3.204  -17.079 -0.310  -7.108  -1.092 0.470  C8  VL5 25 
VL5 N1  N1  N 0 1 N N N N N N 0.735   -14.604 -0.852  -11.530 -1.838 -0.014 N1  VL5 26 
VL5 N23 N2  N 0 1 N N N N N N -6.144  -16.669 -9.404  1.468   3.314  -0.280 N23 VL5 27 
VL5 N26 N3  N 0 1 Y N N N N N -7.747  -15.940 -11.630 4.915   2.447  -1.010 N26 VL5 28 
VL5 N28 N4  N 0 1 N N N N N N -8.575  -14.722 -13.570 7.205   2.501  -1.658 N28 VL5 29 
VL5 N33 N5  N 0 1 N N N N N N -8.305  -18.252 -7.800  3.603   0.399  0.006  N33 VL5 30 
VL5 N38 N6  N 0 1 N N N N N N -9.133  -19.732 -4.521  4.679   -3.166 0.278  N38 VL5 31 
VL5 N7  N7  N 0 1 N N N N N N -1.915  -17.121 0.053   -7.959  -0.917 -0.600 N7  VL5 32 
VL5 N9  N8  N 0 1 N N N N N N -4.118  -17.221 0.553   -7.392  -1.970 1.391  N9  VL5 33 
VL5 O16 O1  O 0 1 N N N N N N -4.664  -16.273 -5.703  -2.426  1.967  0.862  O16 VL5 34 
VL5 O20 O2  O 0 1 N N N N N N -2.524  -15.237 -9.290  -1.801  5.247  1.724  O20 VL5 35 
VL5 O21 O3  O 0 1 N N N N N N -3.269  -17.227 -9.839  -0.168  3.888  2.333  O21 VL5 36 
VL5 O22 O4  O 0 1 N N N N N N -5.419  -16.972 -8.411  0.222   2.720  0.035  O22 VL5 37 
VL5 O32 O5  O 0 1 N N N N N N -6.899  -19.580 -8.928  1.405   0.619  0.234  O32 VL5 38 
VL5 O40 O6  O 0 1 N N N N N N -10.739 -17.784 -6.952  3.756   -0.027 2.587  O40 VL5 39 
VL5 O41 O7  O 0 1 N N N N N N -9.660  -18.539 -4.140  5.784   -3.935 -0.293 O41 VL5 40 
VL5 O43 O8  O 0 1 N N N N N N -10.575 -18.946 -1.886  4.698   -6.102 -0.654 O43 VL5 41 
VL5 O44 O9  O 0 1 N N N N N N -10.124 -16.662 -2.628  7.029   -5.936 -0.347 O44 VL5 42 
VL5 O45 O10 O 0 1 N N N N N N -8.305  -18.094 -2.145  5.412   -5.431 1.491  O45 VL5 43 
VL5 S29 S1  S 0 1 Y N N N N N -9.916  -16.954 -12.550 5.617   4.802  -1.526 S29 VL5 44 
VL5 S42 S2  S 0 1 N N N N N N -9.681  -18.061 -2.674  5.801   -5.399 0.124  S42 VL5 45 
VL5 H1  H1  H 0 1 N N N N N N -1.605  -17.169 -2.502  -5.245  -1.188 2.421  H1  VL5 46 
VL5 H2  H2  H 0 1 N N N N N N -2.239  -16.793 -4.857  -3.193  0.155  2.587  H2  VL5 47 
VL5 H3  H3  H 0 1 N N N N N N -6.297  -16.172 -3.649  -4.178  2.132  -1.075 H3  VL5 48 
VL5 H4  H4  H 0 1 N N N N N N -5.659  -16.530 -1.291  -6.229  0.790  -1.254 H4  VL5 49 
VL5 H5  H5  H 0 1 N N N N N N -3.486  -17.608 -6.768  -2.995  3.630  -0.225 H5  VL5 50 
VL5 H6  H6  H 0 1 N N N N N N -2.799  -15.962 -6.558  -2.105  2.386  -1.136 H6  VL5 51 
VL5 H7  H7  H 0 1 N N N N N N -4.692  -15.068 -7.977  -0.720  4.425  -0.653 H7  VL5 52 
VL5 H8  H8  H 0 1 N N N N N N -0.614  -15.839 -1.894  -10.003 -0.991 1.153  H8  VL5 53 
VL5 H9  H9  H 0 1 N N N N N N 0.599   -16.704 -0.891  -10.472 -0.043 -0.279 H9  VL5 54 
VL5 H10 H10 H 0 1 N N N N N N -0.526  -16.003 1.151   -8.998  -2.716 -0.311 H10 VL5 55 
VL5 H11 H11 H 0 1 N N N N N N -9.596  -18.589 -10.642 3.185   5.244  -0.902 H11 VL5 56 
VL5 H12 H12 H 0 1 N N N N N N -8.905  -20.233 -7.641  2.616   -1.447 0.132  H12 VL5 57 
VL5 H13 H13 H 0 1 N N N N N N -6.643  -18.874 -4.449  4.659   -0.675 -2.023 H13 VL5 58 
VL5 H14 H14 H 0 1 N N N N N N -6.390  -18.636 -6.211  5.457   -2.262 -2.132 H14 VL5 59 
VL5 H15 H15 H 0 1 N N N N N N -7.585  -17.624 -5.330  3.684   -2.164 -2.010 H15 VL5 60 
VL5 H16 H16 H 0 1 N N N N N N -7.124  -21.325 -4.885  6.117   -1.173 1.366  H16 VL5 61 
VL5 H17 H17 H 0 1 N N N N N N -8.437  -21.776 -6.025  6.878   -1.683 -0.160 H17 VL5 62 
VL5 H18 H18 H 0 1 N N N N N N -6.906  -21.074 -6.650  6.080   -0.096 -0.051 H18 VL5 63 
VL5 H19 H19 H 0 1 N Y N N N N -11.065 -19.708 -6.534  3.638   -2.002 2.461  H19 VL5 64 
VL5 H20 H20 H 0 1 N N N N N N -2.595  -14.627 -0.621  -9.755  -0.811 -2.573 H20 VL5 65 
VL5 H21 H21 H 0 1 N N N N N N -2.571  -14.697 1.174   -8.835  -2.326 -2.741 H21 VL5 66 
VL5 H22 H22 H 0 1 N N N N N N -0.481  -13.418 1.232   -11.250 -2.634 -3.300 H22 VL5 67 
VL5 H23 H23 H 0 1 N N N N N N -1.710  -12.525 0.274   -10.762 -3.613 -1.895 H23 VL5 68 
VL5 H24 H24 H 0 1 N N N N N N 0.486   -12.509 -0.872  -12.151 -0.896 -1.786 H24 VL5 69 
VL5 H25 H25 H 0 1 N N N N N N -0.726  -13.432 -1.823  -12.915 -2.470 -1.461 H25 VL5 70 
VL5 H26 H26 H 0 1 N N N N N N 1.248   -14.605 0.006   -11.406 -2.763 0.370  H26 VL5 71 
VL5 H27 H27 H 0 1 N N N N N N -9.354  -14.780 -14.194 7.952   3.052  -1.942 H27 VL5 72 
VL5 H28 H28 H 0 1 N N N N N N -8.589  -13.839 -13.101 7.319   1.543  -1.560 H28 VL5 73 
VL5 H29 H29 H 0 1 N N N N N N -8.533  -17.304 -7.579  4.446   0.793  -0.267 H29 VL5 74 
VL5 H30 H30 H 0 1 N N N N N N -9.887  -20.348 -4.750  4.679   -3.226 1.285  H30 VL5 75 
VL5 H31 H31 H 0 1 N N N N N N -1.500  -18.014 0.227   -7.747  -0.264 -1.286 H31 VL5 76 
VL5 H32 H32 H 0 1 N N N N N N -3.748  -17.358 1.472   -8.203  -2.499 1.323  H32 VL5 77 
VL5 H33 H33 H 0 1 N N N N N N -1.924  -15.426 -10.002 -1.798  5.616  2.618  H33 VL5 78 
VL5 H34 H34 H 0 1 N N N N N N -10.078 -19.361 -1.191  4.621   -7.047 -0.461 H34 VL5 79 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
_chem_comp_bond.pdbx_aromatic_flag 
_chem_comp_bond.pdbx_stereo_config 
_chem_comp_bond.pdbx_ordinal 
VL5 N28 C27 SING N N 1  
VL5 C27 S29 SING Y N 2  
VL5 C27 N26 DOUB Y N 3  
VL5 S29 C30 SING Y N 4  
VL5 N26 C25 SING Y N 5  
VL5 C30 C25 DOUB Y N 6  
VL5 C25 C24 SING N N 7  
VL5 O21 C19 DOUB N N 8  
VL5 C24 N23 DOUB N Z 9  
VL5 C24 C31 SING N N 10 
VL5 N23 O22 SING N N 11 
VL5 O20 C19 SING N N 12 
VL5 C19 C18 SING N N 13 
VL5 O32 C31 DOUB N N 14 
VL5 C31 N33 SING N N 15 
VL5 O22 C18 SING N N 16 
VL5 C18 C17 SING N N 17 
VL5 N33 C34 SING N N 18 
VL5 C34 C39 SING N N 19 
VL5 C34 C35 SING N N 20 
VL5 O40 C39 DOUB N N 21 
VL5 C17 O16 SING N N 22 
VL5 C37 C35 SING N N 23 
VL5 O16 C13 SING N N 24 
VL5 C35 C36 SING N N 25 
VL5 C35 N38 SING N N 26 
VL5 N38 O41 SING N N 27 
VL5 C13 C12 DOUB Y N 28 
VL5 C13 C14 SING Y N 29 
VL5 O41 S42 SING N N 30 
VL5 C12 C11 SING Y N 31 
VL5 C14 C15 DOUB Y N 32 
VL5 C11 C10 DOUB Y N 33 
VL5 S42 O44 DOUB N N 34 
VL5 S42 O45 DOUB N N 35 
VL5 S42 O43 SING N N 36 
VL5 C15 C10 SING Y N 37 
VL5 C10 C8  SING N N 38 
VL5 C2  N1  SING N N 39 
VL5 C2  C3  SING N N 40 
VL5 C6  N1  SING N N 41 
VL5 C6  C5  SING N N 42 
VL5 C8  N7  SING N N 43 
VL5 C8  N9  DOUB N N 44 
VL5 N7  C3  SING N N 45 
VL5 C3  C4  SING N N 46 
VL5 C4  C5  SING N N 47 
VL5 C11 H1  SING N N 48 
VL5 C12 H2  SING N N 49 
VL5 C14 H3  SING N N 50 
VL5 C15 H4  SING N N 51 
VL5 C17 H5  SING N N 52 
VL5 C17 H6  SING N N 53 
VL5 C18 H7  SING N N 54 
VL5 C2  H8  SING N N 55 
VL5 C2  H9  SING N N 56 
VL5 C3  H10 SING N N 57 
VL5 C30 H11 SING N N 58 
VL5 C34 H12 SING N N 59 
VL5 C36 H13 SING N N 60 
VL5 C36 H14 SING N N 61 
VL5 C36 H15 SING N N 62 
VL5 C37 H16 SING N N 63 
VL5 C37 H17 SING N N 64 
VL5 C37 H18 SING N N 65 
VL5 C39 H19 SING N N 66 
VL5 C4  H20 SING N N 67 
VL5 C4  H21 SING N N 68 
VL5 C5  H22 SING N N 69 
VL5 C5  H23 SING N N 70 
VL5 C6  H24 SING N N 71 
VL5 C6  H25 SING N N 72 
VL5 N1  H26 SING N N 73 
VL5 N28 H27 SING N N 74 
VL5 N28 H28 SING N N 75 
VL5 N33 H29 SING N N 76 
VL5 N38 H30 SING N N 77 
VL5 N7  H31 SING N N 78 
VL5 N9  H32 SING N N 79 
VL5 O20 H33 SING N N 80 
VL5 O43 H34 SING N N 81 
# 
loop_
_pdbx_chem_comp_descriptor.comp_id 
_pdbx_chem_comp_descriptor.type 
_pdbx_chem_comp_descriptor.program 
_pdbx_chem_comp_descriptor.program_version 
_pdbx_chem_comp_descriptor.descriptor 
VL5 InChI            InChI                1.03  "InChI=1S/C25H34N8O10S2/c1-25(2,33-43-45(38,39)40)19(11-34)31-22(35)20(17-13-44-24(27)30-17)32-42-18(23(36)37)12-41-16-7-5-14(6-8-16)21(26)29-15-4-3-9-28-10-15/h5-8,11,13,15,18-19,28,33H,3-4,9-10,12H2,1-2H3,(H2,26,29)(H2,27,30)(H,31,35)(H,36,37)(H,38,39,40)/b32-20-/t15-,18+,19-/m1/s1" 
VL5 InChIKey         InChI                1.03  NFNVPYWCKFTXAX-OOLKDPNPSA-N                                                                                                                                                                                                                                                                   
VL5 SMILES_CANONICAL CACTVS               3.385 "CC(C)(NO[S](O)(=O)=O)[C@H](NC(=O)C(=N\O[C@@H](COc1ccc(cc1)C(=N)N[C@@H]2CCCNC2)C(O)=O)/c3csc(N)n3)C=O"                                                                                                                                                                                        
VL5 SMILES           CACTVS               3.385 "CC(C)(NO[S](O)(=O)=O)[CH](NC(=O)C(=NO[CH](COc1ccc(cc1)C(=N)N[CH]2CCCNC2)C(O)=O)c3csc(N)n3)C=O"                                                                                                                                                                                               
VL5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(/c1ccc(cc1)OC[C@@H](C(=O)O)O/N=C(/c2csc(n2)N)\C(=O)N[C@H](C=O)C(C)(C)NOS(=O)(=O)O)\N[C@@H]3CCCNC3"                                                                                                                                                                                   
VL5 SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)(C(C=O)NC(=O)C(=NOC(COc1ccc(cc1)C(=N)NC2CCCNC2)C(=O)O)c3csc(n3)N)NOS(=O)(=O)O"                                                                                                                                                                                                          
# 
_pdbx_chem_comp_identifier.comp_id           VL5 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "(2~{S})-2-[(~{Z})-[1-(2-azanyl-1,3-thiazol-4-yl)-2-[[(2~{S})-3-methyl-1-oxidanylidene-3-(sulfooxyamino)butan-2-yl]amino]-2-oxidanylidene-ethylidene]amino]oxy-3-[4-[~{N}-[(3~{R})-piperidin-3-yl]carbamimidoyl]phenoxy]propanoic acid" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      VL5 
_pdbx_chem_comp_synonyms.name         "AIC499 (bound)" 
_pdbx_chem_comp_synonyms.provenance   AUTHOR 
_pdbx_chem_comp_synonyms.type         ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
VL5 "Create component" 2021-05-27 PDBE 
VL5 "Initial release"  2021-08-04 RCSB 
VL5 "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            VL5 
_pdbx_chem_comp_pcm.modified_residue_id                SER 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               C39 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   OG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
